Biomolecules

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1. Biomolecules

2. Carbon

3. Carbon Bonding

4. Carbohydrates

5. Lipids

6. Proteins

7. Nucleic acids
 1. Biomolecules

The large molecules necessary for life that are built from smaller organic molecules are called biomolecules (also called biological macromolecules).
There are four major classes of biomolecules (carbohydrates, lipids, proteins, and nucleic acids), and each is an important component of the cell and
performs a wide array of functions. Combined, these molecules make up the majority of a cell’s mass. Biomolecules are organic, meaning that they
contain carbon (with some exceptions, like carbon dioxide). In addition, they may contain hydrogen, oxygen, nitrogen, phosphorus, sulphur, and
additional minor elements.
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 2. Carbon

It is often said that life is “carbon-based.” This means that carbon atoms, bonded to other carbon atoms or other elements, form the fundamental
components of many, if not most, of the molecules found uniquely in living things. Other elements play important roles in biological molecules, but
carbon certainly qualifies as the “foundation” element for molecules in living things. It is the bonding properties of carbon atoms that are responsible
for its important role.
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 3. Carbon Bonding

Carbon contains four electrons in its outer shell. Therefore, it can form four covalent bonds with other atoms or molecules. The simplest organic
carbon molecule is methane (CH4), in which four hydrogen atoms bind to a carbon atom (Figure 2.11).

Figure 2.11 Carbon can form four covalent bonds to create an organic molecule. The simplest carbon molecule is methane (CH4), depicted here.
However, structures that are more complex are made using carbon. Any of the hydrogen atoms can be replaced with another carbon atom covalently
bonded to the first carbon atom. In this way, long and branching chains of carbon compounds can be made (Figure 3.13a). The carbon atoms may bond
with atoms of other elements, such as nitrogen, oxygen, and phosphorus (Figure 3.13b). The molecules may also form rings, which themselves can link
with other rings (Figure 3.13c). This diversity of molecular forms accounts for the diversity of functions of the biomolecules and is based to a large
degree on the ability of carbon to form multiple bonds with itself and other atoms.

Figure 2.12 These examples show three molecules (found in living organisms) that contain carbon atoms bonded in various ways to other carbon
atoms and the atoms of other elements. (a) This molecule of stearic acid (a lipid) has a long chain of carbon atoms. (b) Glycine, a component of
proteins, contains carbon, nitrogen, oxygen, and hydrogen atoms. (c) Glucose, a sugar, has a ring of carbon atoms and one oxygen atom.
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 4. Carbohydrates

Carbohydrates are biomolecules with which most consumers are somewhat familiar. To lose weight, some individuals adhere to “low-carb” diets.
Athletes, in contrast, often “carb-load” before important competitions to ensure that they have sufficient energy to compete at a high level.
Carbohydrates are, in fact, an essential part of our diet; grains, fruits, and vegetables are all natural sources of carbohydrates. Carbohydrates provide
energy to the body, particularly through glucose, a simple sugar. Carbohydrates also have other important functions in humans, animals, and plants.

Carbohydrates can be represented by the formula (CH2O)n, where n is the number of carbon atoms in the molecule. In other words, the ratio of carbon
to hydrogen to oxygen is 1:2:1 in carbohydrate molecules. Carbohydrates are classified into three subtypes: monosaccharides, disaccharides, and
polysaccharides.

Monosaccharides (mono- = “one”; sacchar- = “sweet”) are simple sugars, the most common of which is glucose. In monosaccharides, the number of
carbon atoms usually ranges from three to six. Most monosaccharide names end with the suffix -ose. Depending on the number of carbon atoms in the
sugar, they may be known as trioses (three carbon atoms), pentoses (five carbon atoms), and hexoses (six carbon atoms).

Monosaccharides may exist as a linear chain or as ring-shaped molecules; in aqueous solutions, they are usually found in the ring form.

The chemical formula for glucose is C6H12O6. In most living species, glucose is an important source of energy. During cellular respiration, energy is
released from glucose, and that energy is used to help make adenosine triphosphate (ATP). Plants synthesize glucose using carbon dioxide and water
by the process of photosynthesis, and the glucose, in turn, is used for the energy requirements of the plant. The excess synthesized glucose is often
stored as starch that is broken down by other organisms that feed on plants.

Galactose (part of lactose, or milk sugar) and fructose (found in fruit) are other common monosaccharides. Although glucose, galactose, and fructose
all have the same chemical formula (C6H12O6), they differ structurally and chemically (and are known as isomers) because of differing arrangements of
atoms in the carbon chain (Figure 2.13).

Figure 2.13 Glucose, galactose, and fructose are isomeric monosaccharides, meaning that they have the same chemical formula but slightly different
structures.

Disaccharides (di- = “two”) form when two monosaccharides undergo a dehydration reaction (a reaction in which the removal of a water molecule
occurs). During this process, the hydroxyl group (–OH) of one monosaccharide combines with a hydrogen atom of another monosaccharide, releasing
a molecule of water (H2O) and forming a covalent bond between atoms in the two sugar molecules.

Common disaccharides include lactose, maltose, and sucrose. Lactose is a disaccharide consisting of the monomers glucose and galactose. It is found
naturally in milk. Maltose, or malt sugar, is a disaccharide formed from a dehydration reaction between two glucose molecules. The most common
disaccharide is sucrose, or table sugar, which is composed of the monomers glucose and fructose.

A long chain of monosaccharides linked by covalent bonds is known as a polysaccharide (poly- = “many”). The chain may be branched or
unbranched, and it may contain different types of monosaccharides. Polysaccharides may be very large molecules. Starch, glycogen, cellulose, and
chitin are examples of polysaccharides.

Starch is the stored form of sugars in plants and is made up of amylose and amylopectin (both polymers of glucose). Plants are able to synthesize
glucose, and the excess glucose is stored as starch in different plant parts, including roots and seeds. The starch that is consumed by animals is
broken down into smaller molecules, such as glucose. The cells can then absorb the glucose.
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Glycogen is the storage form of glucose in humans and other vertebrates and is made up of monomers of glucose. Glycogen is the animal equivalent
of starch and is a highly branched molecule usually stored in liver and muscle cells. Whenever glucose levels decrease, glycogen is broken down to
release glucose.

Cellulose is one of the most abundant natural biopolymers. The cell walls of plants are mostly made of cellulose, which provides structural support to
the cell. Wood and paper are mostly cellulosic in nature. Cellulose is made up of glucose monomers that are linked by bonds between particular carbon
atoms in the glucose molecule.

Thus, through differences in molecular structure, carbohydrates are able to serve the very different functions of energy storage (starch and
glycogen) and structural support and protection (cellulose and chitin) (Figure 2.14).

Figure 2.14 Although their structures and functions differ, all polysaccharide carbohydrates are made up of monosaccharides and have the chemical
formula (CH2O)n.
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 5. Lipids

Lipids include a diverse group of compounds that are united by a common feature. Lipids are hydrophobic (“water-fearing”), or insoluble in water,
because they are nonpolar molecules. This is because they are hydrocarbons that include only nonpolar carbon-carbon or carbon-hydrogen bonds.
Lipids perform many different functions in a cell. Cells store energy for long-term use in the form of lipids called fats. Lipids also provide insulation
from the environment for plants and animals (Figure 2.15). For example, they help keep aquatic birds and mammals dry because of their water-
repelling nature. Lipids are also the building blocks of steroid hormones (ex- estrogen, testosterone, cortisol) and are an important constituent of the
plasma membrane. Lipids include fats, oils, phospholipids, and steroids.

Figure 2.15 Hydrophobic lipids in the fur of aquatic mammals, such as this river otter, protect them from the elements. (Credit: Ken Bosma)

A fat molecule, such as a triglyceride, consists of two main components—glycerol and fatty acids. Glycerol is an organic compound with three carbon
atoms, five hydrogen atoms, and three hydroxyl (–OH) groups. Fatty acids have a long chain of hydrocarbons to which an acidic carboxyl group is
attached, hence the name “fatty acid.” The number of carbons in the fatty acid may range from 4 to 36; most common are those containing 12–18
carbons. In a fat molecule, a fatty acid is attached to each of the three oxygen atoms in the –OH groups of the glycerol molecule with a covalent bond
(Figure 2.16).

Figure 2.16 Lipids include fats, such as triglycerides, which are made up of fatty acids and glycerol, phospholipids, and steroids.
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During this covalent bond formation, three water molecules are released. The three fatty acids in the fat may be similar or dissimilar. These fats are
also called triglycerides because they have three fatty acids. Some fatty acids have common names that specify their origin. For example, palmitic
acid, a saturated fatty acid, is derived from the palm tree. Arachidic acid is derived from Arachis hypogaea, the scientific name for peanuts.

Fatty acids may be saturated or unsaturated. In a fatty acid chain, if there are only single bonds between neighbouring carbons in the hydrocarbon
chain, the fatty acid is saturated. Saturated fatty acids are saturated with hydrogen; in other words, the number of hydrogen atoms attached to the
carbon skeleton is maximized.

When the hydrocarbon chain contains a double bond, the fatty acid is an unsaturated fatty acid.

Most unsaturated fats are liquid at room temperature and are called oils. If there is one double bond in the molecule, then it is known as a
monounsaturated fat (e.g., olive oil), and if there is more than one double bond, then it is known as a polyunsaturated fat (e.g., canola oil).

Saturated fats tend to get packed tightly and are solid at room temperature. Animal fats with stearic acid and palmitic acid contained in meat, and the
fat with butyric acid contained in butter, are examples of saturated fats. Mammals store fats in specialized cells called adipocytes, where globules of
fat occupy most of the cell. In plants, fat or oil is stored in seeds and is used as a source of energy during embryonic development.

Unsaturated fats or oils are usually of plant origin and contain unsaturated fatty acids. The double bond causes a bend or a “kink” that prevents the
fatty acids from packing tightly, keeping them liquid at room temperature. Olive oil, corn oil, canola oil, and cod liver oil are examples of unsaturated
fats. Unsaturated fats help to improve blood cholesterol levels, whereas saturated fats contribute to plaque formation in the arteries, which increases
the risk of a heart attack.

In the food industry, oils are artificially hydrogenated to make them semi-solid, leading to less spoilage and increased shelf life. Simply speaking,
hydrogen gas is bubbled through oils to solidify them. During this hydrogenation process, double bonds of the cis-conformation in the hydrocarbon
chain may be converted to double bonds in the trans-conformation. This forms a trans-fat from a cis-fat. The orientation of the double bonds affects
the chemical properties of the fat (Figure 2.17).

Figure 2.17 During the hydrogenation process, the orientation around the double bonds is changed, making a trans-fat from a cis-fat. This changes
the chemical properties of the molecule.

Margarine, some types of peanut butter, and shortening are examples of artificially hydrogenated trans-fats. Recent studies have shown that an
increase in trans-fats in the human diet may lead to an increase in levels of low-density lipoprotein (LDL), or “bad” cholesterol, which, in turn, may lead
to plaque deposition in the arteries, resulting in heart disease. Many fast-food restaurants have recently eliminated the use of trans-fats, and U.S. food
labels are now required to list their trans-fat content.

Essential fatty acids are fatty acids that are required but not synthesized by the human body. Consequently, they must be supplemented through the
diet. Omega-3 fatty acids fall into this category and are one of only two known essential fatty acids for humans (the other being omega-6 fatty acids).
They are a type of polyunsaturated fat and are called omega-3 fatty acids because the third carbon from the end of the fatty acid participates in a
double bond.

Salmon, trout, and tuna are good sources of omega-3 fatty acids. Omega-3 fatty acids are important in brain function and normal growth and
development. They may also prevent heart disease and reduce the risk of cancer.

Like carbohydrates, fats have received a lot of bad publicity. It is true that eating an excess of fried foods and other “fatty” foods leads to weight gain.
However, fats do have important functions. Fats serve as long-term energy storage. They also provide insulation for the body. Therefore, “healthy”
unsaturated fats in moderate amounts should be consumed on a regular basis.

Phospholipids (Figure 2.18) are the major constituent of the plasma membrane. Like fats, they are composed of fatty acid chains attached to a
glycerol or similar backbone. Instead of three fatty acids attached, however, there are two fatty acids, and the third carbon of the glycerol backbone is
bound to a phosphate group. The phosphate group is modified by the addition of an alcohol.

A phospholipid has both hydrophobic and hydrophilic regions. The fatty acid chains are hydrophobic and exclude themselves from water, whereas the
phosphate is hydrophilic and interacts with water.
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Figure 2.18 A phospholipid is a molecule with two fatty acids and a modified phosphate group attached to a glycerol backbone. Adding a charged or
polar chemical group may modify the phosphate. (Credit Openstax Biology 2e)

Cells are surrounded by a membrane, which has a bilayer of phospholipids (Figure 2.19). The fatty acids of phospholipids face inside, away from water,
whereas the phosphate group can face either the outside environment or the inside of the cell, which are both aqueous.

Figure 2.19 The phospholipid bilayer is the major component of all cellular membranes. The hydrophilic head groups of the phospholipids face the
aqueous solution. The hydrophobic tails are sequestered in the middle of the bilayer. (Credit Openstax Biology 2e)

Steroids

Unlike the phospholipids and fats discussed earlier, steroids have a ring structure (Figure 3.21). Although they do not resemble other lipids, they are
grouped with them because they are also hydrophobic. All steroids have four, linked carbon rings and several of them, like cholesterol, have a short
tail.

Cholesterol is a steroid. Cholesterol is mainly synthesized in the liver and is the precursor of many steroid hormones, such as testosterone and
estradiol. It is also the precursor of vitamins E and K. Cholesterol is the precursor of bile salts, which help in the breakdown of fats and their
subsequent absorption by cells. Although cholesterol is often spoken of in negative terms, it is necessary for the proper functioning of the body. It is a
key component of the plasma membranes of animal cells.
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Figure 2.20 Four fused hydrocarbon rings comprise steroids such as cholesterol and cortisol.
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 6. Proteins

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all biomolecules. Proteins
may be structural, regulatory, contractile, or protective; they may serve in transport, storage, or membranes; or they may be toxins or enzymes. Each
cell in a living system may contain thousands of different proteins, each with a unique function. Their structures, like their functions, vary greatly. They
are all, however, polymers of amino acids, arranged in a linear sequence.

The functions of proteins are very diverse because there are 20 different chemically distinct amino acids that form long chains, and the amino acids
can be in any order. For example, proteins can function as enzymes or hormones. Enzymes, which are produced by living cells, are catalysts in
biochemical reactions (like digestion) and are usually proteins. Each enzyme is specific for the substrate (a reactant that binds to an enzyme) upon
which it acts. Enzymes can function to break molecular bonds, to rearrange bonds, or to form new bonds. An example of an enzyme is salivary
amylase, which breaks down amylose, a component of starch.

Hormones are chemical signalling molecules, usually proteins or steroids, secreted by an endocrine gland or group of endocrine cells that act to
control or regulate specific physiological processes, including growth, development, metabolism, and reproduction. For example, insulin is a protein
hormone that maintains blood glucose levels.

Proteins have different shapes and molecular weights; some proteins are globular in shape whereas others are fibrous in nature. For example,
haemoglobin is a globular protein, but collagen, found in our skin, is a fibrous protein. Protein shape is critical to its function. Changes in temperature,
pH, and exposure to chemicals may lead to permanent changes in the shape of the protein, leading to a loss of function or denaturation (to be
discussed in more detail later). All proteins are made up of different arrangements of the same 20 kinds of amino acids.

Amino acids are the monomers that make up proteins. Each amino acid has the same fundamental structure, which consists of a central carbon atom
bonded to an amino group (–NH2), a carboxyl group (–COOH), and a hydrogen atom. Every amino acid also has another variable atom or group of
atoms bonded to the central carbon atom known as the R group. The R group is the only difference in structure between the 20 amino acids; otherwise,
the amino acids are identical (Figure 2.21).
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Figure 2.21 Amino acids are made up of a central carbon bonded to an amino group (–NH2), a carboxyl group (–COOH), and a hydrogen atom. The
central carbon’s fourth bond varies among the different amino acids, as seen in these examples of alanine, valine, lysine, and aspartic acid.

The chemical nature of the R group determines the chemical nature of the amino acid within its protein (that is, whether it is acidic, basic, polar, or
nonpolar).

The sequence and number of amino acids ultimately determine a protein’s shape, size, and function. Each amino acid is attached to another amino acid
by a covalent bond, known as a peptide bond, which is formed by a dehydration reaction. The carboxyl group of one amino acid and the amino group
of a second amino acid combine, releasing a water molecule. The resulting bond is the peptide bond.

The products formed by such a linkage are called polypeptides. While the terms polypeptide and protein are sometimes used interchangeably, a
polypeptide is technically a polymer of amino acids, whereas the term protein is used for a polypeptide or polypeptides that have combined together,
have a distinct shape, and have a unique function.

Protein Structure

As discussed earlier, the shape (structure) of a protein is critical to its function. To understand how the protein gets its final shape or
conformation, we need to understand the four levels of protein structure: primary, secondary, tertiary, and quaternary (Figure 2.22).

The unique sequence and number of amino acids in a polypeptide chain is its primary structure. The unique sequence for every protein is ultimately
determined by the gene that encodes the protein. Any change in the gene sequence may lead to a different amino acid being added to the
polypeptide chain, causing a change in protein structure and function. In sickle cell anaemia, the haemoglobin β chain has a single amino acid
substitution, causing a change in both the structure and function of the protein. What is most remarkable to consider is that a haemoglobin molecule is
made up of two alpha chains and two beta chains that each consist of about 150 amino acids. The molecule, therefore, has about 600 amino acids. The
structural difference between a normal haemoglobin molecule and a sickle cell molecule—that dramatically decreases life expectancy in the affected
individuals—is a single amino acid of the 600.
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Because of this change of one amino acid in the chain, the normally biconcave, or disc-shaped, red blood cells assume a crescent or “sickle” shape,
which clogs arteries. This can lead to a myriad of serious health problems, such as breathlessness, dizziness, headaches, and abdominal pain for those
who have this disease.

Folding patterns resulting from interactions between the non-R group portions of amino acids give rise to the secondary structure of the protein. The
most common are the alpha (α)-helix and beta (β)-pleated sheet structures. Both structures are held in shape by hydrogen bonds. In the alpha
helix, the bonds form between every fourth amino acid and cause a twist in the amino acid chain.

The unique three-dimensional structure of a polypeptide is known as its tertiary structure. This structure is caused by chemical interactions between
various amino acids and regions of the polypeptide. Primarily, the interactions among R groups create the complex three-dimensional tertiary structure
of a protein. There may be ionic bonds formed between R groups on different amino acids, or hydrogen bonding beyond that involved in the secondary
structure. When protein folding takes place, the hydrophobic R groups of nonpolar amino acids lay in the interior of the protein, whereas the
hydrophilic R groups lay on the outside. The former types of interactions are also known as hydrophobic interactions.

In nature, some proteins are formed from several polypeptides, also known as subunits, and the interaction of these subunits forms the quaternary
structure. Weak interactions between the subunits help to stabilize the overall structure. For example, haemoglobin is a combination of four
polypeptide subunits.

Figure 2.22 The four levels of protein structure can be observed in these illustrations. (Credit: modification of work by National Human Genome
Research Institute)
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 7. Nucleic acids

Nucleic acids are key biomolecules in the continuity of life. They carry the genetic blueprint of a cell and carry instructions for the functioning of the
cell.

The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material found in all living
organisms, ranging from single-celled bacteria to multicellular mammals.

DNA and RNA are made up of monomers known as nucleotides. The nucleotides combine with each other to form a polynucleotide, DNA or RNA. Each
nucleotide is made up of three components: a nitrogenous base, a pentose (five-carbon) sugar, and a phosphate group (Figure 2.23). Each nitrogenous
base in a nucleotide is attached to a sugar molecule, which is attached to a phosphate group.

Figure 2.23 A nucleotide is made up of three components: a nitrogenous base, a pentose sugar, and a phosphate group.

DNA Double-Helical Structure

DNA has a double-helical structure (Figure 2.24). It is composed of two strands, or polymers, of nucleotides. The strands are formed with bonds
between phosphate and sugar groups of adjacent nucleotides. The strands are bonded to each other at their bases with hydrogen bonds, and the
strands coil about each other along their length, hence the “double helix” description, which means a double spiral.
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Figure 2.24 The double-helix model shows DNA as two parallel strands of intertwining molecules. (Credit: Jerome Walker, Dennis Myts)

The alternating sugar and phosphate groups lie on the outside of each strand, forming the backbone of the DNA. The nitrogenous bases are stacked in
the interior, like the steps of a staircase, and these bases pair; the pairs are bound to each other by hydrogen bonds. The bases pair in such a way that
the distance between the backbones of the two strands is the same all along the molecule.
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